Genetic characterization of type A foot-and-mouth disease virus 3A region in context of the reemergence of VP359-deletion lineage in India

Infection, Genetics and Evolution

Volumn 9, Issue 4, 2009, Pages 483-492

  Mohapatra, Jajati Keshari ^a   Sahu, Abhipsa ^a   Pandey, Laxmikant ^a   Sanyal, Aniket ^a   Hemadri, Divakar ^a   Pattnaik, Bramhadev ^a  

^a Indian Veterinary Research Institute Campus   (India)

Author keywords

3A region; FMD virus; Genomics; Serotype A; VP359 deletion lineage

Indexed keywords

AMINO ACID; PROTEIN VP3; VIRUS RNA;

AMINO ACID SUBSTITUTION; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; FOOT AND MOUTH DISEASE VIRUS; FOOT AND MOUTH DISEASE VIRUS TYPE A; GENE DELETION; GENE MUTATION; GENETIC ANALYSIS; GENOTYPE; GUINEA PIG; HOST PATHOGEN INTERACTION; INDIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POSITION EFFECT; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN RNA BINDING; VIRAL GENETICS; VIRUS VIRULENCE;

AMINO ACID SEQUENCE; ANIMALS; CAPSID PROTEINS; CATTLE; CATTLE DISEASES; FOOT-AND-MOUTH DISEASE; FOOT-AND-MOUTH DISEASE VIRUS; INDIA; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SELECTION (GENETICS); SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; SEROTYPING;

CAVIA; FOOT-AND-MOUTH DISEASE VIRUS; MIRIDAE;

EID: 68949108006     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2009.01.009     Document Type: Article

References (38)

1. Beard C.W., and Mason P.W. Genetic determinants of altered virulence of Taiwanese foot-and-mouth disease virus. J. Virol. 74 (2000) 987-991
2. Bienz K., Egger D., Rasser Y., and Bossart W. Intracellular distribution of poliovirus proteins and the induction of virus-specific cytoplasmic structures. Virology 131 (1983) 39-48
3. Biswas S., Sanyal A., Hemadri D., Tosh C., Mohapatra J.K., Manoj R., and Bandyopadhyay S.K. Sequence analysis of the non-structural 3A and 3C protein-coding regions of foot-and-mouth disease virus serotype Asia 1 field isolates from an endemic country. Vet. Microbiol. 116 (2006) 187-193
4. Blanco E., Garcia-Briones M., Sanz-Parra A., Gomes P., De Oliveira E., Valero M.L., Andreu D., Ley V., and Sobrino F. Identification of T-cell epitopes in nonstructural proteins of foot-and-mouth disease virus. J. Virol. 75 (2001) 3164-3174
5. Carrillo C., Tulman E.R., Delhon G., Lu Z., Carreno A., Vagnozzi A., Kutish G.F., and Rock D.L. Comparative genomics of foot-and-mouth disease virus. J. Virol. 79 (2005) 6487-6504
6. Claros M.G., and Heijne G.v. TopPred II: an improved software for membrane protein structure predictions. Comput. Appl. Biosci. 10 (1994) 685-686
7. Doedens J.R., Giddings Jr. T.H., and Kirkegaard K. Inhibition of endoplasmic reticulum-to-Golgi traffic by poliovirus protein 3A: genetic and ultrastructural analysis. J. Virol. 71 (1997) 9054-9064
8. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
9. Giraudo A.T., Beck E., Strebel K., de Mello P.A., La Torre J.L., Scodeller E.A., and Bergmann I.E. Identification of a nucleotide deletion in parts of polypeptide 3A in two independent attenuated aphthovirus strains. Virology 177 (1990) 780-783
10. Giraudo A.T., Sagedahl A., Bergmann I.E., La Torre J.L., and Scodeller E.A. Isolation and characterization of recombinants between attenuated and virulent aphthovirus strains. J. Virol. 61 (1987) 419-425
11. Hofmann K., and Stoffel W. TMBASE-a database of membrane spanning protein segments. Biol. Chem. Hoppe-Seyler 374 (1993) 166
12. Hohlich B., Wiesmuller K., Schlapp T., Haas B., Pfaff E., and Saalmuller A. Identification of foot-and-mouth disease virus-specific linear B-cell epitopes to differentiate between infected and vaccinated cattle. J. Virol. 77 (2003) 8633-8639
13. Jangra R.K., Tosh C., Sanyal A., Hemadri D., and Bandyopadhyay S.K. Antigenic and genetic analyses of foot-and-mouth disease virus type A isolates for selection of candidate strain reveals emergence of a variant virus that is responsible for most recent outbreaks in India. Virus Res. 112 (2005) 52-59
14. Juretic D., and Jeroncic A. Sequence analysis of membrane proteins with the web server SPLIT. Croat. Chem. Acta 77 (1999) 975-997
15. Knowles N.J., Davies P.R., Henry T., O'Donnell V., Pacheco J.M., and Mason P.W. Emergence in Asia of foot-and-mouth disease viruses with altered host range: characterization of alterations in the 3A protein. J. Virol. 75 (2001) 1551-1556
16. Knox C., Moffat K., Ali S., Ryan M., and Wileman T. Foot-and-mouth disease virus replication sites form next to the nucleus and close to the Golgi apparatus, but exclude marker proteins associated with host membrane compartments. J. Gen. Virol. 86 (2005) 687-696
17. Kosakovsky Pond S.L., and Frost S.D.W. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21 10 (2005) 2531-2533
18. Krogh A., Larsson B., Heijne G.V., and Sonnhammer E.L.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305 (2001) 567-580
19. Mittal M., Tosh C., Hemadri D., Sanyal A., and Bandyopadhyay S.K. Phylogeny, genome evolution, and antigenic variability among endemic foot-and-mouth disease virus type A isolates from India. Arch. Virol. 150 (2005) 911-928
20. Mohapatra J.K., Hemadri D., Rao T.V.S., Sreenivasa B.P., Subramaniam S., Sanyal A., Periyasamy T.R., Singh N.K., Pattnaik B., and Venkataramanan R. Assessment of suitability of two serotype A candidate vaccine strains for inclusion in FMD vaccine in India. Vet. Microbiol. 131 (2008) 65-72
21. Mohapatra J.K., Sanyal A., Hemadri D., Tosh C., Biswas S., Rasool T.J., Bandyopadhyay S.K., and Pattnaik B. Comparative genomics of serotype Asia 1 foot-and-mouth disease virus isolates from India sampled over the last two decades. Virus Res. 136 (2008) 16-29
22. Monaghan P., Cook H., Jackson T., Ryan M., and Wileman T. The ultrastructure of the developing replication site in foot-and-mouth disease virus-infected BHK-38 cells. J. Gen. Virol. 85 (2004) 933-946
23. Nobiron I., Remond M., Kaiser C., Lebreton F., Zientara S., and Delmas B. The nucleotide sequence of foot-and-mouth disease virus O/FRA/1/2001 and comparison with its British parental strain O/UKG/35/2001. Virus Res. 108 (2005) 225-229
24. Nunez J.I., Baranowski E., Molina N., Ruiz-Jarabo C.M., Sanchez C., Domingo E., and Sobrino F. A single amino acid substitution in nonstructural protein 3A can mediate adaptation of foot-and-mouth disease virus to the guinea pig. J. Virol. 75 (2001) 3977-3983
25. Nunez J.I., Molina N., Baranowski E., Domingo E., Clark S., Burman A., Berryman S., Jackson T., and Sobrino F. Guinea pig-adapted foot-and-mouth disease virus with altered receptor recognition can productively infect a natural host. J. Virol. 81 (2007) 8497-8506
26. O'Donnell V.K., Pacheco J.M., Henry T.M., and Mason P.W. Subcellular distribution of the foot-and-mouth disease virus 3A protein in cells infected with viruses encoding wild-type and bovine-attenuated forms of 3A. Virology 287 (2001) 151-162
27. Pacheco J.M., Henry T.M., O'Donnell V.K., Gregory J.B., and Mason P.W. Role of nonstructural proteins 3A and 3B in host range and pathogenicity of foot-and-mouth disease virus. J. Virol. 77 (2003) 13017-13027
28. Ray, S.C., 1999. SimPlot for Windows 95, version 2.5. Distributed by the author 641 (www.med.jhu.edu/deptmed/sray/download).
29. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. 4 (1987) 406-425
30. Tamura K., Dudley J., Nei M., and Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. (2007) 10.1093/molbev/msm092
31. Tamura K., and Kumar S. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol. Biol. Evol. 19 (2002) 1727-1736
32. Tamura K., and Nei M. Estimation of the number of nucleotide substitution in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 (1993) 512-526
33. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
34. Tosh C., Sanyal A., Hemadri D., and Venkataraman R. Phylogenetic analysis of serotype A foot-and-mouth disease virus isolated in India between 1977 and 2000. Arch. Virol. 147 (2002) 493-513
35. Tusnady G.E., and Simon I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol. 283 (1998) 489-506
36. Van Rensberg H., Haydon D., Joubert F., Bastos A., and Heath L. Genetic heterogeneity in the foot-and-mouth disease virus leader and 3C proteinases. Gene 289 (2002) 19-29
37. Yang Z.H. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24 (2007) 1586-1591
38. Yang Z.H., Nielsen R., Goldman N., and Pedersen A.M.K. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155 (2000) 431-449